Contacts of the helix formed by residues 69 - 75 (chain A) in PDB entry 4PEI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY* 2.9 23.0 + - - +
18A LYS* 4.1 5.3 + - - +
19A TYR* 3.5 19.0 + - + +
20A ARG* 2.8 56.7 + - - +
21A GLU 4.4 0.7 + - - -
68A GLY* 1.3 71.6 - - - -
70A PHE* 1.3 68.8 + - - +
71A HIS* 3.2 4.0 - - - -
72A LEU* 2.9 27.4 + - - +
73A TYR* 3.7 6.0 - - + -
403A GOL 3.3 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY* 4.9 0.2 - - - -
19A TYR* 3.8 25.4 - + + -
47A GLN 3.6 21.0 + - - +
48A THR* 3.4 32.8 - - + -
49A LEU 3.5 19.7 - - - +
50A ARG* 4.7 2.5 - - + -
67A MET 4.6 1.3 + - - +
68A GLY 3.6 2.0 - - - -
69A ASP* 1.3 78.7 - - - +
71A HIS* 1.3 63.4 + - - +
73A TYR* 2.9 19.1 + - + +
74A TYR* 2.9 37.7 + + + -
106A VAL* 3.6 48.7 - - + -
107A CYS* 3.9 17.0 - - - -
110A MET* 4.0 7.6 - - - -
333A PHE* 5.9 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU 3.7 12.1 + - - +
50A ARG 3.5 22.0 - - - +
67A MET* 4.1 20.3 + - + +
68A GLY 3.2 21.8 - - - -
69A ASP 3.0 1.0 + - - -
70A PHE* 1.3 78.8 - - - +
72A LEU* 1.3 77.1 + - + +
74A TYR* 3.5 8.0 - - - +
75A GLU* 2.8 62.5 + - - +
403A GOL 2.8 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.6 47.6 - - + +
69A ASP* 2.9 13.2 + - - +
71A HIS* 1.3 123.3 - - + +
73A TYR* 1.3 59.6 + - + +
75A GLU* 3.5 9.4 + - - +
76A GLY 3.1 5.4 + - - -
77A LYS* 2.9 42.4 + - + +
78A GLU* 3.2 21.8 + - + +
403A GOL 3.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.4 26.7 - - + -
20A ARG* 3.4 30.3 - - + +
23A TYR* 3.5 27.4 - + - +
69A ASP* 3.7 16.8 - - + -
70A PHE* 2.9 9.6 + - + +
72A LEU* 1.3 74.7 - - + +
74A TYR* 1.3 66.0 + - - +
75A GLU 3.1 0.4 - - - -
76A GLY* 3.2 12.3 + - - -
78A GLU* 3.5 35.9 + - + +
79A LYS 3.9 3.6 - - - -
80A ALA 3.6 28.5 - - - -
107A CYS* 3.9 28.2 - - - +
108A PHE 5.3 0.7 + - - -
110A MET* 3.7 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.8 51.8 + - + -
51A TYR* 4.4 14.7 + + - -
70A PHE* 2.9 26.2 + + + +
71A HIS* 3.5 11.4 - - - +
73A TYR* 1.3 77.7 - - - +
75A GLU* 1.3 66.5 + - + +
76A GLY 3.6 0.3 + - - -
106A VAL 3.5 17.3 - - - -
107A CYS* 4.1 10.3 - - + +
332A THR* 5.2 12.1 - - - +
333A PHE* 3.9 20.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG 4.6 3.6 - - - +
71A HIS* 2.8 54.3 + - - +
72A LEU* 3.8 5.7 - - - +
73A TYR 3.1 0.2 - - - -
74A TYR* 1.3 86.4 - - + +
76A GLY* 1.3 58.7 + - - +
77A LYS* 3.4 36.7 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il